knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
knitr::opts_chunk$set(echo = F, warning = F, message = F)

p014ot0

Data loading and qc

Velocyto counts are loaded

Data Filtering

## $cluster_res
## [1] 2
## 
## $sample_name
## [1] "p014ot0"
## 
## $loom_file
## [1] "_data/_patients/velocyto/p014ot0.loom"
## 
## $nFeature_lower
## [1] 500
## 
## $nFeature_upper
## [1] 5000
## 
## $nCount_lower
## [1] 1000
## 
## $nCount_upper
## [1] 50000
## 
## $nFrac_s_lower
## [1] 0.3
## 
## $nFrac_s_upper
## [1] 0.9
## 
## $nFrac_u_lower
## [1] 0.1
## 
## $nFrac_u_upper
## [1] 0.7
## 
## $nFrac_a_lower
## [1] 0
## 
## $nFrac_a_upper
## [1] 0.2
## 
## $pMT_lower
## [1] 0
## 
## $pMT_upper
## [1] 0.8
## 
## $pHB_lower
## [1] 0
## 
## $pHB_upper
## [1] 0.1
## 
## $rel_comp
## [1] 10

Before filtering

## An object of class Seurat 
## 100542 features across 21590 samples within 3 assays 
## Active assay: spliced (33514 features)
##  2 other assays present: unspliced, ambiguous

After filtering

## An object of class Seurat 
## 100542 features across 18463 samples within 3 assays 
## Active assay: spliced (33514 features)
##  2 other assays present: unspliced, ambiguous

Data normalisation

Cell cycle scoring

Data scaling and dimensionality reduction

Elbow plot

Cell cycle phase

Cell type identification

Louvain clusters

Cluster marker genes

rank 0 1 10 12 13 14 15 16 17 18 19 2 20 21 22 23 24 25 26 3 4 5 6 7 8 9
1 NEAT1 RPS2 FABP6 RPS2 HIST1H4C TFF1 HIST1H4C PHGR1 CCL20 CENPF SPRR3 FTL FOS CXCL1 LGALS1 STC1 GDF15 KRT19 TFF1 FABP1 PTMA CCL20
2 MALAT1 RPLP1 ADIRF RPLP1 HMGB2 REG4 HIST1H1D FABP1 CXCL1 PTTG1 KLK10 S100P HES1 CCL20 VIM PECAM1 HLA-A LGALS4 FABP1 PHGR1 RPS2 CXCL1
3 MUC2 RPS18 UGT2B17 RPS19 TYMS KRT8 UBE2C LGALS3 RPS2 PTMA REG4 ADIRF RPS2 CXCL3 IGFBP7 VIM MUC13 FABP1 PHGR1 S100A6 HSP90AB1 CXCL8
4 DDX5 RPS19 ANPEP RPS12 HIST1H1D KRT18 TOP2A S100A6 CXCL3 MKI67 KRT18 TPT1 RPLP1 CXCL8 MGP TCF4 FTH1 TXN S100A6 LGALS3 H2AFZ MUC13
5 PLEC RPS12 FABP2 RPS18 CLSPN KRT19 HMGB2 ADIRF PTMA HMGB2 PI3 MALAT1 RPS4X CXCL2 SPARC GNG11 CEACAM6 AGR2 IFI27 LGALS4 HMGB1 TM4SF1
6 FAT1 RPS27 HSD17B2 RPL32 GINS2 AGR2 CDK1 LGALS4 RPS19 CCNB1 CEACAM6 SPINK1 RPL3 NFKBIA BGN SPARC LCN2 ETHE1 REG4 KRT19 MT1E SQSTM1
7 RPL6 FXYD3 RPL3 HIST1H1B S100A16 NUSAP1 ABCG2 RPLP1 HMGB1 TSPAN8 MDK RPS19 TM4SF1 CAV1 SOX18 SPINK1 PHLDA2 TSPAN8 ANXA10 RPS19 AREG
8 RPL12 SLC40A1 RPL13A HIST1H3B TFF3 H2AFZ KRT20 RPS6 HSP90AB1 GPRC5A IFI27 RPS6 AREG COL1A2 CD93 HLA-C S100A16 LGALS3 S100A10 RPLP1 PI3
9 AGR2 SLC26A3 RPL6 FAM111B MUC2 TYMS SULT1B1 RPS18 DLGAP5 GSTP1 SERPINE2 IER3 SQSTM1 FN1 EGFL7 SQSTM1 ANXA10 ADIRF KRT8 MT2A CLDN3
10 RPL3 MTTP RPS6 CENPU TFF2 PBK HPGD RPS12 H2AFZ PLAC8 HLA-A RPL23 CLDN3 THY1 RFLNB TPT1 AKR1C3 FXYD3 KRT20 TUBA1B KLK10
11 RPL32 ABCG2 MT1E TOP2A ANXA10 BIRC5 AKR1C3 RPS27 TOP2A KLK7 RPL12 RPL7A MUC13 COL3A1 MCAM CD55 SERPINB1 LGALS4 TSPAN8 RPS6 PLAC8
12 RPL13A PHGR1 RPS27 HIST1H1E MKI67 TM4SF4 RPS4X NCL SLPI SAT1 RPSA TMSB4X COL6A2 GJA1 DDIT3 KRT20 SERPINB6 NPM1 SPRR3
13 RPS14 FABP1 RPL10A BRCA2 CENPU MALAT1 RPS27A HSP90AA1 S100A10 PPDPF RPS3A PI3 CALD1 COL4A1 AREG SLPI S100A16 TMSB10 TSPAN1
14 RPS6 FTL RPL12 TK1 HMMR FABP2 RPL5 RPS2 TSPAN1 MMP1 RPL10A GDF15 PLAC9 ESM1 TMSB4X TM4SF4 ETHE1 HSPD1 MUC2
15 RPS4X TM4SF4 RPS14 GMNN UBE2T IFI27 TMSB10 NUCKS1 KRT23 MYH4 RPL11 MUC2 COL6A3 PLVAP PI3 CEACAM6 S100A11 RPL6 MAL2
16 RPL10A C10orf99 RPSA H2AFZ TUBA1B ANPEP RPS3A TUBA1B MAL2 SLC40A1 LYZ IER3 C11orf96 TM4SF18 MALAT1 TFF2 DHRS9 RPS12 GDF15
17 RPS3A AKR1B10 RPLP2 CDK1 TUBB FTL RPL7A HSPD1 AREG EIF1 RPL5 KLK10 SFRP1 CRIP2 SAT1 HSD17B2 PHLDA2 NCL
18 RPL5 IFI27 PTMA PTMA CENPF EPCAM RPS8 YBX1 MUC13 EIF2S2 PTMA LCN2 BEX3 ADGRF5 CLDN4 S100P SH3BGRL3 RPL35
19 RPS8 PCK1 RPL13 HELLS CKS2 AKR1B10 RPL6 MT1E CD9 TMBIM6 CLDN2 TCEAL9 KDR HLA-E AKR1B10 AKR1C3 YBX1
20 RPSA SULT1B1 RPS27A MAD2L1 PTMA SLC22A18 RPL13A NPM1 LGALS3 ZFAS1 RPS8 GNG11 A2M TSPAN1 HPGD CD9 NASP
21 RPLP2 SMIM24 RPL21 TUBA1B HMGB1 TMEM54 RPL10A ANP32B SH3BGRL3 FTH1 RPS12 CYGB CLEC14A TMC5 CTSE SERPINB1 LDHB
22 RPS3 HPGD TMSB10 PCNA PCNA ETHE1 RPL3 CKS2 CD55 SYF2 RPS27A COL18A1 CLDN5 UBC SH3BGRL3 GUCA2A RPSA
23 RPLP0 LGALS4 RPS16 MKI67 MAD2L1 SRI RPSA SERBP1 ADGRF1 TMEM59 RPL13A PDGFRB CLEC2B RAB11FIP1 TFF3 REG4 ANP32B
24 RPL21 AKR1C3 RPS3 UBE2T RANBP1 CXCL8 LDHB TM4SF4 CAMK2N1 RPS3 MCAM PXDN MUC2 SLC22A18 KRT18 PTTG1
25 RPS9 C2orf88 RPS3A RAD51AP1 PTTG1 RPS15A HNRNPM KLK6 HLA-C RPS27 COX7A1 FLT1 ABHD2 EPCAM S100A14 RPS27A
26 C3orf85 RPS4X NASP DTYMK NPM1 HNRNPAB TM4SF1 LCN2 NAP1L1 ANTXR1 ENG KLK10 SMIM22 TXNDC17 RPS18
27 SLC51B RPS8 DUT DUT YBX1 PTGES3 CLDN3 RPS7 MAP1B ACKR3 JUN ANXA10 TMEM54 RPS27
28 MEP1A RPS7 RFC3 NASP RPL35A SRSF3 CLIC1 DUSP1 NOTCH3 SPARCL1 CLDN3 ISG20 ABCG2 RPL10A
29 CBR1 RPL35 HMGB1 RPA3 LDHB HNRNPA2B1 ANXA3 RPL13 SERPINE1 GIMAP4 OCIAD2 MMP1 HPGD RPL5
30 LGALS3 RPL19 PBK KPNA2 RPS5 ENO1 TMC5 LDHB EMP3 CDH5 FOS DHRS9 JPT1 RPL13A
31 PSCA RPLP0 UBE2C MT2A MT1E DEK EPCAM AQP5 TUBA1A GIMAP7 IER2 RHOC ARL14 RPL3
32 CD36 RPL37 CENPM MT1E RPL23 RAN SFN ID3 PLAU RDX MMP1 CAMK2N1 ISG20 RPS4X
33 CEACAM7 RPL5 MCM6 NUCKS1 H2AFZ RPL22L1 DHRS9 EGR1 CCDC102B CALCRL SCD ATP2B1 ENO1
34 ITM2B NACA MCM7 H1FX NAP1L1 NAP1L1 KRT20 GDF15 PLAT IQCA1 SERPINB6 TM4SF4 NUCKS1
35 DHRS11 GAPDH ZWINT LDHB RPLP0 TUBB MUC2 YBX1 COL6A1 CYTL1 MGST3 GMNN
36 TSPAN8 RPL11 BIRC5 DEK RPS3 CLDN4 RPL6 STC1 TNFRSF4 SLC9A3R1 GAPDH
37 UQCRQ RPL7A MT2A SNRPG MT2A ABHD2 RPS5 SELENOM PCDH17 DNAJC15 HSP90AA1
38 S100A6 RPL36 TUBB RAN PKM TFF2 TSC22D1 TAGLN EMCN DSC2 RPL32
39 CAMK2N1 RPL35A NUSAP1 TUBB4B HSP90AB1 LMO7 JUN COL1A1 TCEAL4 RANBP1
40 TXNIP RPS24 RRM1 NPM1 HIST1H4C LMO4 RPS15A SPON2 NBDY RPS3
41 SRI RPS5 MT1E HNRNPDL HMGB1 SLC12A2 ACTA2 HEY1 RPS5
42 OAT RPS15A RANBP1 HSPD1 RPL21 MT1E NR2F1 ADAMTS1 RPLP2
43 CES2 RPL18A RPS2 SRSF3 ENO1 RPS9 IFITM3 CAV1 RPL7A
44 DHRS7 HMGB1 PTTG1 RPL22L1 RPL22L1 IL33 CAVIN3 ANGPT2 RPL19
45 CTSE RPL23 DNMT1 SNRPF SLC25A6 RPL4 TIMP1 CXCR4 RPS16
46 COX6C NPM1 LDHB HNRNPAB NUCKS1 IER2 COL4A2 RGCC RAN
47 GHITM HSP90AB1 DTYMK NCL SNRPD2 PKM TMEM158 BEX3 RPL22L1
48 CDHR5 RPL28 NPM1 ANP32B SNRPF ID1 MFGE8 MEF2C NAP1L1
49 CEACAM6 RPL34 CENPF NAP1L1 TUBA1B RPL22L1 NR2F2 LGALS1 RPS3A
50 ALDH1A1 RPS29 YBX1 IER3 LCN2 TFPI NRP1 SNRPF
51 SPPL2A RPL8 BTG3 KANK2 WWTR1 RPL8
52 AOC1 RPL37A SMC2 TPM2 ELK3 PCNA
53 MALAT1 RPL23A MCM3 S100A4 FAM198B RPL23A
54 COX7B RPS28 H2AFX RARRES2 HTRA1 RPL23
55 CRYL1 RPS23 TPX2 ZFP36L1 IGFBP3 RPL13
56 ATP1B1 LDHB KIF20B CD81 COL4A2 RPS7
57 HSPB1 RPS20 ANP32B ANXA5 IFITM3 RPL36
58 FAM213A YBX1 NCL MT2A BCAM SERBP1
59 PRR15 MT2A NUCKS1 ID4 CTGF RPL21
60 SLC22A18 RPL24 USP1 TLN1 PGM2L1 RPS15A
61 CA2 RPL10 NAP1L1 CD63 CAVIN1 RPL35A
62 GUCA2A NAP1L1 PSIP1 DSTN FABP5 RPS23
63 GPA33 RPS11 DEK ITGB1 ARRDC3 RPS20
64 EPCAM RPS15 RPS19 IGFBP2 SPRY1 RPS15
65 SAT1 RPL27 HSPD1 PNRC1 NDST1 RPL18A
66 DUSP1 AGR2 HSP90AB1 TUBA1B INSR SNHG19
67 NDUFA1 RPL31 TMSB10 ID3 PLK2 RPLP0
68 SELENOW RPL30 CDK4 CEBPB CAV2 HNRNPM
69 SMIM22 ENO1 RAN EID1 CDC42EP3 NACA
70 CDH17 RPS9 SMC4 MARCKS LAMC1 CENPF
71 PRR13 RPL18 SNRPF EPS8 UNC5B DEK
72 FUOM EEF1B2 ENO1 HLA-E RPL27
73 SCP2 RPL22L1 FBL CYR61 HNRNPA2B1
74 PRDX6 HSPD1 RPLP1 HLA-C SNRPD1
75 JUN NCL AQP5 IVNS1ABP PKM
76 LIMA1 RPL7 RPS6 HLA-A HSPE1
77 SLPI RPL22 H1FX ITM2B SNRPG
78 MGST3 H2AFZ RPSA POMP RPL7
79 TST SNRPD2 RPS3A EFNA1 SET
80 ECHS1 SERBP1 RPS4X ARHGAP29 HNRNPDL
81 PIGR MT1G EZH2 CD81 EEF1B2
82 ANP32B SIVA1 SPTBN1 SRSF3
83 NUCKS1 HSP90AA1 YBX3 PTGES3
84 SNRPF RPL22L1 SH3BP5 MT1G
85 GAPDH SNX3 RPS9
86 RPA3 TMSB4X SNRPD2
87 DBF4 EMP1 RPL4
88 SUPT16H JAK1 NAA38
89 SRSF3 BTG1 HNRNPAB
90 RPS27A CALM1 RPL22
91 SNRPD1 FOSB TUBB
92 RPS3 SMAD1 HMGN1
93 RPL5 TSC22D1 SRSF7
94 RPS12 ARHGAP18 LSM7
95 RPS8 PPP1R15A HMGA1
96 SERBP1 ETS2 SLC25A6
97 PAICS XPC LSM5
98 HNRNPD B2M HNRNPK
99 RPL35 DARS EIF5A
100 SNRPG MYO10 C1QBP
NA no_sig_genes no_sig_genes no_sig_genes no_sig_genes

separation of epithelial, stromal and immune cells

Cell split